StudyType	PubMedID	Author	Title	Journal	PublishDate	Chromosome	Disease	Technology	Species	CaseID	Platform	CNA	Connection	Gene	Affiliation	Abstract	GenomeAssembly	GEO	dbGaP	ENA	IsCancer	FusionGene
Research	24819516	Iannelli F, Collino A, Sinha S, Radaelli E, Nicoli P, D'Antiga L, Sonzogni A, Faivre J, Buendia MA, Sturm E, Thompson RJ, Knisely AS, Natoli G, Ghisletti S, Ciccarelli FD	Massive gene amplification drives paediatric hepatocellular carcinoma caused by bile salt export pump deficiency	Nature Communications	2014 May 	4,6	Hepatocellular carcinoma	SNP Array	Homo sapiens	UKT	Illumina HumanOmniExpress-12 v1.0	chr10:0-4431609:0;chr10:10185316-10228683:0;chr10:10228684-10586371:1;chr10:10586372-47681956:0;chr10:117395006-117727166:1;chr10:117727167-135534747:0;chr10:4431610-4944816:1;chr10:47681957-47940417:1;chr10:47940418-52451271:0;chr10:4944817-8563174:0;chr10:52451272-58121201:1;chr10:58121202-58249478:0;chr10:58249479-60590203:1;chr10:60590204-66827629:0;chr10:66827630-67780727:1;chr10:67780728-67780897:0;chr10:67780898-70455490:1;chr10:70455491-82653859:0;chr10:82653860-85210888:1;chr10:85210889-85210945:0;chr10:85210946-85241941:-1;chr10:85241942-117395005:0;chr10:8563175-10185315:1;chr11:0-135006516:0;chr12:0-85071585:0;chr12:85071586-85091700:1;chr12:85091701-133851895:0;chr13:0-51542208:0;chr13:115103530-115169878:0;chr13:51542209-115103529:1;chr14:0-25281567:0;chr14:25281568-30102025:1;chr14:30102026-40314469:0;chr14:40314470-49384358:1;chr14:49384359-71092255:0;chr14:71092256-71117483:-1;chr14:71117484-79399654:0;chr14:79399655-85693853:1;chr14:85693854-85709381:0;chr14:85709382-88494613:1;chr14:88494614-107349540:0;chr15:0-26824731:0;chr15:26824732-26865632:1;chr15:26865633-80315415:0;chr15:80315416-80331233:-1;chr15:80331234-102531392:0;chr16:0-46450036:0;chr16:46450037-58900866:-1;chr16:58900867-65596701:0;chr16:65596702-72147186:-1;chr16:72147187-80913668:0;chr16:80913669-82181608:-1;chr16:82181609-82181976:0;chr16:82181977-82182229:1;chr16:82182230-90354753:0;chr17:0-32354752:0;chr17:32354753-32501774:-1;chr17:32501775-50577943:0;chr17:50577944-53248927:1;chr17:53248928-77365872:0;chr17:77365873-77368132:1;chr17:77368133-81195210:0;chr18:0-24384539:0;chr18:24384540-29146918:1;chr18:29146919-37707850:0;chr18:37707851-42306884:1;chr18:42306885-56872177:0;chr18:56872178-56878274:1;chr18:56878275-62191652:0;chr18:62191653-67718688:1;chr18:67718689-68585023:0;chr18:68585024-71412693:1;chr18:71412694-78077248:0;chr19:0-260911:0;chr19:11879420-18502835:1;chr19:18502836-19902915:0;chr19:19902916-29343037:1;chr19:260912-7266944:1;chr19:29343038-29347038:0;chr19:29347039-34309277:1;chr19:34309278-34333500:0;chr19:34333501-36856251:1;chr19:36856252-36856378:0;chr19:36856379-38702777:1;chr19:38702778-50741569:0;chr19:50741570-53518747:1;chr19:53518748-53554239:0;chr19:53554240-54720958:1;chr19:54720959-55859438:0;chr19:55859439-58141281:1;chr19:58141282-58153576:0;chr19:58153577-59097160:1;chr19:59097161-59128983:0;chr19:7266945-11879419:0;chr1:0-7811960:0;chr1:100043790-102297844:0;chr1:102297845-108421058:1;chr1:108421059-165646757:0;chr1:165646758-165650616:1;chr1:165650617-184527030:0;chr1:184527031-193700387:1;chr1:193700388-193715322:0;chr1:193715323-197521877:1;chr1:197521878-214751785:0;chr1:214751786-217088584:1;chr1:217088585-237773426:0;chr1:237773427-242158192:1;chr1:242158193-249250621:0;chr1:46989742-46990681:-1;chr1:46990682-68407583:0;chr1:68407584-76499313:1;chr1:76499314-79174954:0;chr1:7811961-7829107:1;chr1:7829108-46989741:0;chr1:79174955-84917707:1;chr1:84917708-96339893:0;chr1:96339894-100043789:1;chr20:0-63243:0;chr20:13954880-14031391:0;chr20:14031392-17459584:1;chr20:1726904-1727506:0;chr20:1727507-1729560:1;chr20:1729561-1748125:0;chr20:17459585-17463916:0;chr20:17463917-24639916:1;chr20:1748126-6087162:1;chr20:24639917-24666099:0;chr20:24666100-26293985:1;chr20:26293986-29445643:0;chr20:29445644-52845398:1;chr20:52845399-52851118:0;chr20:52851119-54784952:1;chr20:54784953-54795922:0;chr20:54795923-56965708:1;chr20:56965709-57032712:0;chr20:57032713-57357395:1;chr20:57357396-57374242:0;chr20:57374243-59971800:1;chr20:59971801-59988068:0;chr20:59988069-62764435:1;chr20:6087163-6089740:0;chr20:6089741-9051482:1;chr20:62764436-63025520:0;chr20:63244-1726903:1;chr20:9051483-9055819:0;chr20:9055820-9088624:1;chr20:9088625-9109892:0;chr20:9109893-13954879:1;chr21:0-10827532:0;chr21:10827533-23250041:1;chr21:23250042-23264429:0;chr21:23264430-26699228:1;chr21:26699229-26706355:0;chr21:26706356-27922192:1;chr21:27922193-27924202:0;chr21:27924203-32485200:1;chr21:32485201-32486882:0;chr21:32486883-46926551:1;chr21:46926552-46934860:0;chr21:46934861-48100155:1;chr21:48100156-48129895:0;chr22:0-51304566:0;chr2:0-4237883:0;chr2:14255030-14255040:0;chr2:14255041-14286717:1;chr2:14286718-81313892:0;chr2:209140046-243199373:0;chr2:4237884-5488456:1;chr2:5488457-5488518:0;chr2:5488519-14255029:1;chr2:81313893-81440526:1;chr2:81440527-81444319:0;chr2:81444320-209140045:1;chr3:0-3191812:0;chr3:3191813-3207754:1;chr3:3207755-198022430:0;chr4:0-27268341:0;chr4:113782927-113784481:0;chr4:113784482-113924858:-1;chr4:113924859-113927364:0;chr4:113927365-138609462:1;chr4:138609463-141410250:0;chr4:141410251-143421175:1;chr4:143421176-143426030:0;chr4:143426031-143452535:1;chr4:143452536-177360668:0;chr4:177360669-178803423:1;chr4:178803424-178805082:0;chr4:178805083-178821372:-1;chr4:178821373-178827896:0;chr4:178827897-183574838:1;chr4:183574839-191154276:0;chr4:27268342-29314598:1;chr4:29314599-29317917:0;chr4:29317918-29330467:1;chr4:29330468-29331116:0;chr4:29331117-31071934:1;chr4:31071935-31077544:0;chr4:31077545-31104796:-1;chr4:31104797-31110336:0;chr4:31110337-36325988:1;chr4:36325989-43232758:0;chr4:43232759-47181795:1;chr4:47181796-58121588:0;chr4:58121589-69822928:1;chr4:69822929-69901662:0;chr4:69901663-70521159:1;chr4:70521160-91046718:0;chr4:91046719-113782926:1;chr5:0-81979165:0;chr5:106276533-115885573:0;chr5:115885574-122514588:1;chr5:122514589-124188886:0;chr5:124188887-124245657:1;chr5:124245658-127740575:0;chr5:127740576-130164900:1;chr5:130164901-162652826:0;chr5:162652827-167070649:1;chr5:167070650-180915260:0;chr5:81979166-84163069:1;chr5:84163070-84167823:0;chr5:84167824-89439105:1;chr5:89439106-89456354:0;chr5:89456355-92141172:1;chr5:92141173-98593452:0;chr5:98593453-106276532:1;chr6:0-7979532:0;chr6:10155288-23978217:0;chr6:104559149-120222328:0;chr6:120222329-123897071:1;chr6:123897072-140219413:0;chr6:140219414-142024463:1;chr6:142024464-148940807:0;chr6:148940808-148997371:-1;chr6:148997372-166287777:0;chr6:166287778-166308198:1;chr6:166308199-171115067:0;chr6:23978218-23984030:-1;chr6:23984031-33110833:0;chr6:33110834-33115762:-1;chr6:33115763-61891117:0;chr6:61891118-65289746:1;chr6:65289747-65317294:0;chr6:65317295-69743528:1;chr6:69743529-91210593:0;chr6:7979533-10155287:1;chr6:91210594-104559148:1;chr7:0-77818151:0;chr7:144137137-147277640:1;chr7:147277641-159138663:0;chr7:77818152-97463961:1;chr7:97463962-144137136:0;chr8:0-164983:0;chr8:105810398-105815144:0;chr8:105815145-115448234:1;chr8:11147124-11406592:0;chr8:11406593-12933568:1;chr8:115448235-115923991:0;chr8:115923992-123537857:1;chr8:123537858-123537947:0;chr8:123537948-126798409:1;chr8:126798410-126799010:0;chr8:126799011-127306602:1;chr8:127306603-127308156:0;chr8:127308157-129043582:1;chr8:129043583-129059109:0;chr8:129059110-134660741:1;chr8:12933569-12933580:0;chr8:12933581-15037929:1;chr8:134660742-134673367:0;chr8:134673368-135792825:1;chr8:135792826-135793641:0;chr8:135793642-135794496:1;chr8:135794497-135796965:0;chr8:135796966-138209669:1;chr8:138209670-138243038:0;chr8:138243039-139101291:1;chr8:139101292-139102266:0;chr8:139102267-146293414:1;chr8:146293415-146364022:0;chr8:15037930-15051871:0;chr8:15051872-15258706:1;chr8:15258707-15265900:0;chr8:15265901-16823648:1;chr8:164984-2290039:1;chr8:16823649-17780035:0;chr8:17780036-19113393:1;chr8:19113394-19121923:0;chr8:19121924-20274088:1;chr8:20274089-20280941:0;chr8:20280942-27856331:1;chr8:2290040-2292023:0;chr8:2292024-4219116:1;chr8:27856332-27858736:0;chr8:27858737-27875050:-1;chr8:27875051-27875619:0;chr8:27875620-30455200:1;chr8:30455201-30462148:0;chr8:30462149-50115532:1;chr8:4219117-4225232:0;chr8:4225233-5172992:1;chr8:50115533-50125077:0;chr8:50125078-51988578:1;chr8:5172993-5182238:0;chr8:5182239-5818128:1;chr8:51988579-51996074:0;chr8:51996075-61979873:1;chr8:5818129-5823185:0;chr8:5823186-11147123:1;chr8:61979874-62000238:0;chr8:62000239-69996372:1;chr8:69996373-70049903:0;chr8:70049904-75239978:1;chr8:75239979-75242410:0;chr8:75242411-77539322:1;chr8:77539323-77718818:0;chr8:77718819-79654145:1;chr8:79654146-80519540:0;chr8:80519541-83265571:1;chr8:83265572-83292294:0;chr8:83292295-90372173:1;chr8:90372174-90520648:0;chr8:90520649-105810397:1;chr9:0-8227100:0;chr9:104443319-107760227:1;chr9:107760228-119939388:0;chr9:119939389-119955982:-1;chr9:119955983-125254954:0;chr9:125254955-125257838:-1;chr9:125257839-141213431:0;chr9:13458524-22159981:0;chr9:22159982-26178732:1;chr9:26178733-28420019:0;chr9:28420020-31856797:1;chr9:31856798-31868611:0;chr9:31868612-31892857:1;chr9:31892858-90051390:0;chr9:8227101-13458523:1;chr9:90051391-90095024:1;chr9:90095025-104443318:0;chrX:0-155270560:0;chrY:0-59373566:0		ADAD1;ADH1A;ADH1B;ADH1C;ADH4;ADH5;ADH6;ADH7;AGA;AGXT2L1;AIMP1;ALPK1;ANKRD50;ANXA5;AP1AR;ARAP2;ARHGEF38;ARSJ;ASCC3;ATOH1;BANK1;BBS12;BBS7;BDH2;BMPR1B;C4orf17;C4orf21;C4orf29;C4orf3;C4orf32;C4orf33;C4orf37;C6orf168;C6orf170;CAMK2D;CASP6;CCDC109B;CCNA2;CCNC;CENPC1;CENPE;CEP170P1;CFI;CISD2;CLVS2;COL25A1;COQ3;COX7B2;CXXC4;CYP2U1;DAPP1;DDIT4L;DKK2;DNAJB14;EEF1E1;EEF1E1-MUTED;EGF;EIF4E;ELMOD2;ELOVL6;EMCN;ENPEP;EPHA5;EPHA7;EXOSC9;FABP2;FABP7;FAM190A;FAT4;FBXL4;FGF2;FHL5;FLJ20021;FTLP10;FUT9;GABRA2;GABRA4;GABRG1;GAR1;GJA1;GNPDA2;GNRHR;GPR63;GRID2;GRIK2;GSTCD;GUF1;H2AFZ;HADH;HPGDS;HSF2;HSPA4L;IL15;IL2;IL21;INPP4B;INTS12;INTU;KCTD8;KHDRBS2;KIAA1109;KLHL32;LAMTOR3;LARP1B;LARP7;LEF1;LGSN;LOC100130890;LOC100507096;LOC285456;LOC285501;LOC550112;LOC641518;LPHN3;LRIT3;MAD2L1;MANBA;MANEA;MAP3K7;MCHR2;METAP1;METTL14;MFSD8;MIR1243;MIR1305;MIR2054;MIR2113;MIR302A;MIR302B;MIR302C;MIR302D;MIR3668;MIR367;MIR3684;MIR4275;MIR4465;MIR4643;MIR577;MMS22L;MTRNR2L9;MTTP;MUTED;MYOZ2;NDNF;NDST3;NDST4;NDUFAF4;NEIL3;NEUROG2;NFKB1;NPNT;NUDT6;OSTC;PABPC4L;PAPSS1;PCDH10;PCDH18;PCDH7;PDE5A;PDHA2;PDLIM5;PGRMC2;PHF17;PHF3;PIP5K1P1;PITX2;PKIB;PLA2G12A;PLK4;PNISR;POU3F2;PP12613;PPA2;PPP3CA;PRDM13;PRDM5;PRSS12;PTP4A1;QRFPR;RAP1GDS1;RG9MTD2;RNF150;RPL34;RRH;SCLT1;SEC24B;SEC24D;SERINC1;SGMS2;SIM1;SLC25A31;SLC35B3;SLC39A8;SLC9B1;SLC9B2;SMARCAD1;SMPDL3A;SNHG8;SPATA5;SPRY1;STAP1;SYNPO2;SYT14L;TACR3;TBC1D9;TBCK;TECRL;TET2;TMEM155;TMPRSS11A;TMPRSS11B;TMPRSS11BNL;TMPRSS11D;TMPRSS11F;TNIP3;TRAM1L1;TRDN;TRPC3;TSPAN5;UBA6;UBE2D3;UCP1;UFL1;UGT2A1;UGT2A2;UGT2A3;UGT2B15;UGT2B17;UGT2B4;UGT2B7;UGT8;UNC5C;USP45;USP53;VEGFC;YIPF7;YTHDC1;ZNF330;	European Institute of Oncology (IEO), Department of Experimental Oncology, IFOM-IEO Campus, Via Adamello 16, 20139 Milan, Italy 	Hepatocellular carcinoma (HCC) is almost invariably associated with an underlying inflammatory state, whose direct contribution to the acquisition of critical genomic changes is unclear. Here we map acquired genomic alterations in human and mouse HCCs induced by defects in hepatocyte biliary transporters, which expose hepatocytes to bile salts and cause chronic inflammation that develops into cancer. In both human and mouse cancer genomes, we find few somatic point mutations with no impairment of cancer genes, but massive gene amplification and rearrangements. This genomic landscape differs from that of virus- and alcohol-associated liver cancer. Copy-number gains preferentially occur at late stages of cancer development and frequently target the MAPK signalling pathway, and in particular direct regulators of JNK. The pharmacological inhibition of JNK retards cancer progression in the mouse. Our study demonstrates that intrahepatic cholestasis leading to hepatocyte exposure to bile acids and inflammation promotes cancer through genomic modifications that can be distinguished from those determined by other aetiological factors. 	GRCh37/hg19				Yes	NA
Research	24819516	Iannelli F, Collino A, Sinha S, Radaelli E, Nicoli P, D'Antiga L, Sonzogni A, Faivre J, Buendia MA, Sturm E, Thompson RJ, Knisely AS, Natoli G, Ghisletti S, Ciccarelli FD	Massive gene amplification drives paediatric hepatocellular carcinoma caused by bile salt export pump deficiency	Nature Communications	2014 May 	19	Hepatocellular carcinoma	Next Generation Sequencing	Mus musculus	60400/1	Illumina Genome Analyzer Iix and Illumina 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Institute of Oncology (IEO), Department of Experimental Oncology, IFOM-IEO Campus, Via Adamello 16, 20139 Milan, Italy 	Hepatocellular carcinoma (HCC) is almost invariably associated with an underlying inflammatory state, whose direct contribution to the acquisition of critical genomic changes is unclear. Here we map acquired genomic alterations in human and mouse HCCs induced by defects in hepatocyte biliary transporters, which expose hepatocytes to bile salts and cause chronic inflammation that develops into cancer. In both human and mouse cancer genomes, we find few somatic point mutations with no impairment of cancer genes, but massive gene amplification and rearrangements. This genomic landscape differs from that of virus- and alcohol-associated liver cancer. Copy-number gains preferentially occur at late stages of cancer development and frequently target the MAPK signalling pathway, and in particular direct regulators of JNK. The pharmacological inhibition of JNK retards cancer progression in the mouse. Our study demonstrates that intrahepatic cholestasis leading to hepatocyte exposure to bile acids and inflammation promotes cancer through genomic modifications that can be distinguished from those determined by other aetiological factors. 	NCBI37/mm9				Yes	NA